Starting phenix.real_space_refine on Sat Mar 23 16:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq1_32082/03_2024/7vq1_32082.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 24384 2.51 5 N 6680 2.21 5 O 6592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1310": "NH1" <-> "NH2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A ARG 1354": "NH1" <-> "NH2" Residue "A ARG 1356": "NH1" <-> "NH2" Residue "A ARG 1365": "NH1" <-> "NH2" Residue "A ARG 1474": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B ARG 774": "NH1" <-> "NH2" Residue "B PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 896": "NH1" <-> "NH2" Residue "B PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1143": "NH1" <-> "NH2" Residue "B ARG 1310": "NH1" <-> "NH2" Residue "B ARG 1311": "NH1" <-> "NH2" Residue "B ARG 1354": "NH1" <-> "NH2" Residue "B ARG 1356": "NH1" <-> "NH2" Residue "B ARG 1365": "NH1" <-> "NH2" Residue "B ARG 1474": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 316": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 685": "NH1" <-> "NH2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C ARG 774": "NH1" <-> "NH2" Residue "C PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "C PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1143": "NH1" <-> "NH2" Residue "C ARG 1310": "NH1" <-> "NH2" Residue "C ARG 1311": "NH1" <-> "NH2" Residue "C ARG 1354": "NH1" <-> "NH2" Residue "C ARG 1356": "NH1" <-> "NH2" Residue "C ARG 1365": "NH1" <-> "NH2" Residue "C ARG 1474": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 316": "NH1" <-> "NH2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 685": "NH1" <-> "NH2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D ARG 700": "NH1" <-> "NH2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D ARG 774": "NH1" <-> "NH2" Residue "D PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "D PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 896": "NH1" <-> "NH2" Residue "D PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1143": "NH1" <-> "NH2" Residue "D ARG 1310": "NH1" <-> "NH2" Residue "D ARG 1311": "NH1" <-> "NH2" Residue "D ARG 1354": "NH1" <-> "NH2" Residue "D ARG 1356": "NH1" <-> "NH2" Residue "D ARG 1365": "NH1" <-> "NH2" Residue "D ARG 1474": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37804 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 48, 'ASP:plan': 33} Unresolved non-hydrogen planarities: 711 Chain: "B" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 48, 'ASP:plan': 33} Unresolved non-hydrogen planarities: 711 Chain: "C" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 48, 'ASP:plan': 33} Unresolved non-hydrogen planarities: 711 Chain: "D" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 48, 'ASP:plan': 33} Unresolved non-hydrogen planarities: 711 Time building chain proxies: 18.30, per 1000 atoms: 0.48 Number of scatterers: 37804 At special positions: 0 Unit cell: (173.565, 174.42, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 6592 8.00 N 6680 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.33 Conformation dependent library (CDL) restraints added in 6.9 seconds 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9832 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 34 sheets defined 55.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.723A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.760A pdb=" N VAL A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 530 through 542 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.997A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 767 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 855 through 866 Processing helix chain 'A' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 909 removed outlier: 3.532A pdb=" N ARG A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE A 916 " --> pdb=" O ILE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 4.684A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A1095 " --> pdb=" O GLN A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1141 Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 Processing helix chain 'A' and resid 1410 through 1419 Processing helix chain 'A' and resid 1454 through 1463 Processing helix chain 'A' and resid 1485 through 1498 removed outlier: 3.691A pdb=" N LYS A1489 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A1490 " --> pdb=" O ALA A1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.725A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.761A pdb=" N ARG B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.761A pdb=" N VAL B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 363 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 444 Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.667A pdb=" N ASP B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.998A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 663 Processing helix chain 'B' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 705 Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 733 through 744 Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.801A pdb=" N GLN B 779 " --> pdb=" O GLU B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 846 Processing helix chain 'B' and resid 855 through 866 Processing helix chain 'B' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 909 removed outlier: 3.533A pdb=" N ARG B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE B 916 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 4.683A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 979 Processing helix chain 'B' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN B1037 " --> pdb=" O LEU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1056 Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE B1062 " --> pdb=" O HIS B1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B1095 " --> pdb=" O GLN B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1141 Processing helix chain 'B' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1403 Processing helix chain 'B' and resid 1410 through 1419 Processing helix chain 'B' and resid 1454 through 1463 Processing helix chain 'B' and resid 1485 through 1498 removed outlier: 3.692A pdb=" N LYS B1489 " --> pdb=" O TYR B1485 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B1490 " --> pdb=" O ALA B1486 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.723A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG C 304 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 357 through 367 removed outlier: 3.760A pdb=" N VAL C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 444 Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP C 453 " --> pdb=" O HIS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 530 through 542 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.997A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 663 Processing helix chain 'C' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 697 " --> pdb=" O CYS C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 753 through 762 Processing helix chain 'C' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 767 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN C 779 " --> pdb=" O GLU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 846 Processing helix chain 'C' and resid 855 through 866 Processing helix chain 'C' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 909 removed outlier: 3.532A pdb=" N ARG C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE C 916 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 4.684A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 979 Processing helix chain 'C' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN C1037 " --> pdb=" O LEU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1056 Processing helix chain 'C' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE C1062 " --> pdb=" O HIS C1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C1095 " --> pdb=" O GLN C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1141 Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA C1157 " --> pdb=" O ASN C1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1398 through 1403 Processing helix chain 'C' and resid 1410 through 1419 Processing helix chain 'C' and resid 1454 through 1463 Processing helix chain 'C' and resid 1485 through 1498 removed outlier: 3.691A pdb=" N LYS C1489 " --> pdb=" O TYR C1485 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR C1490 " --> pdb=" O ALA C1486 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.724A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 229 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 Processing helix chain 'D' and resid 357 through 367 removed outlier: 3.761A pdb=" N VAL D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 363 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP D 453 " --> pdb=" O HIS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 530 through 543 Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.998A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.683A pdb=" N ALA D 643 " --> pdb=" O GLY D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 663 Processing helix chain 'D' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 Processing helix chain 'D' and resid 716 through 725 Processing helix chain 'D' and resid 726 through 731 Processing helix chain 'D' and resid 733 through 744 Processing helix chain 'D' and resid 753 through 762 Processing helix chain 'D' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU D 766 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 767 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 846 Processing helix chain 'D' and resid 855 through 866 Processing helix chain 'D' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 909 removed outlier: 3.533A pdb=" N ARG D 909 " --> pdb=" O LEU D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 916 removed outlier: 3.518A pdb=" N ILE D 916 " --> pdb=" O ILE D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 4.683A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 979 Processing helix chain 'D' and resid 1021 through 1037 removed outlier: 3.657A pdb=" N ASN D1037 " --> pdb=" O LEU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 Processing helix chain 'D' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE D1062 " --> pdb=" O HIS D1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D1095 " --> pdb=" O GLN D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1141 Processing helix chain 'D' and resid 1143 through 1165 removed outlier: 3.654A pdb=" N ALA D1157 " --> pdb=" O ASN D1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1398 through 1403 Processing helix chain 'D' and resid 1410 through 1419 Processing helix chain 'D' and resid 1454 through 1463 Processing helix chain 'D' and resid 1485 through 1498 removed outlier: 3.692A pdb=" N LYS D1489 " --> pdb=" O TYR D1485 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR D1490 " --> pdb=" O ALA D1486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.464A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 242 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 128 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 264 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1275 through 1277 Processing sheet with id=AA6, first strand: chain 'A' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG A1310 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A1308 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1347 through 1348 Processing sheet with id=AA8, first strand: chain 'A' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1472 " --> pdb=" O LYS A1378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1427 through 1428 removed outlier: 3.767A pdb=" N GLY A1427 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1442 " --> pdb=" O GLY A1427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 68 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.465A pdb=" N ILE B 171 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 242 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 128 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 264 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1275 through 1277 Processing sheet with id=AB6, first strand: chain 'B' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG B1310 " --> pdb=" O VAL B1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B1308 " --> pdb=" O ASP B1305 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 7.044A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B1442 " --> pdb=" O GLY B1427 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B1427 " --> pdb=" O THR B1442 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR B1353 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B1472 " --> pdb=" O LYS B1378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 68 through 72 Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.464A pdb=" N ILE C 171 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 242 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 128 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 264 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AC3, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 1275 through 1277 Processing sheet with id=AC5, first strand: chain 'C' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG C1310 " --> pdb=" O VAL C1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG C1308 " --> pdb=" O ASP C1305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1347 through 1348 Processing sheet with id=AC7, first strand: chain 'C' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR C1353 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C1472 " --> pdb=" O LYS C1378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1427 through 1428 removed outlier: 3.767A pdb=" N GLY C1427 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C1442 " --> pdb=" O GLY C1427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.465A pdb=" N ILE D 171 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 242 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 128 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 264 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 313 through 316 Processing sheet with id=AD3, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AD5, first strand: chain 'D' and resid 1303 through 1305 removed outlier: 3.787A pdb=" N ARG D1310 " --> pdb=" O VAL D1303 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG D1308 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 7.043A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D1442 " --> pdb=" O GLY D1427 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D1427 " --> pdb=" O THR D1442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR D1353 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D1472 " --> pdb=" O LYS D1378 " (cutoff:3.500A) 2022 hydrogen bonds defined for protein. 5910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.33 Time building geometry restraints manager: 15.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12414 1.34 - 1.46: 7980 1.46 - 1.57: 18082 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 38700 Sorted by residual: bond pdb=" CB TRP C 744 " pdb=" CG TRP C 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP A 744 " pdb=" CG TRP A 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP D 744 " pdb=" CG TRP D 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP B 744 " pdb=" CG TRP B 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.48e+00 bond pdb=" CB TRP D 835 " pdb=" CG TRP D 835 " ideal model delta sigma weight residual 1.498 1.417 0.081 3.10e-02 1.04e+03 6.90e+00 ... (remaining 38695 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.20: 1057 106.20 - 113.17: 22353 113.17 - 120.13: 12898 120.13 - 127.10: 16016 127.10 - 134.07: 588 Bond angle restraints: 52912 Sorted by residual: angle pdb=" N VAL B 73 " pdb=" CA VAL B 73 " pdb=" C VAL B 73 " ideal model delta sigma weight residual 113.10 108.15 4.95 9.70e-01 1.06e+00 2.60e+01 angle pdb=" N VAL D 73 " pdb=" CA VAL D 73 " pdb=" C VAL D 73 " ideal model delta sigma weight residual 113.10 108.16 4.94 9.70e-01 1.06e+00 2.59e+01 angle pdb=" N VAL A 73 " pdb=" CA VAL A 73 " pdb=" C VAL A 73 " ideal model delta sigma weight residual 113.10 108.18 4.92 9.70e-01 1.06e+00 2.57e+01 angle pdb=" N VAL C 73 " pdb=" CA VAL C 73 " pdb=" C VAL C 73 " ideal model delta sigma weight residual 113.10 108.18 4.92 9.70e-01 1.06e+00 2.57e+01 angle pdb=" C TYR B 682 " pdb=" N GLU B 683 " pdb=" CA GLU B 683 " ideal model delta sigma weight residual 120.28 115.36 4.92 1.44e+00 4.82e-01 1.17e+01 ... (remaining 52907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 20739 17.47 - 34.95: 1673 34.95 - 52.42: 284 52.42 - 69.89: 68 69.89 - 87.36: 24 Dihedral angle restraints: 22788 sinusoidal: 7652 harmonic: 15136 Sorted by residual: dihedral pdb=" CA ASP C 647 " pdb=" C ASP C 647 " pdb=" N CYS C 648 " pdb=" CA CYS C 648 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP A 647 " pdb=" C ASP A 647 " pdb=" N CYS A 648 " pdb=" CA CYS A 648 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP D 647 " pdb=" C ASP D 647 " pdb=" N CYS D 648 " pdb=" CA CYS D 648 " ideal model delta harmonic sigma weight residual 180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 22785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3736 0.035 - 0.070: 1621 0.070 - 0.105: 648 0.105 - 0.140: 193 0.140 - 0.176: 10 Chirality restraints: 6208 Sorted by residual: chirality pdb=" CA TYR C 682 " pdb=" N TYR C 682 " pdb=" C TYR C 682 " pdb=" CB TYR C 682 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 682 " pdb=" N TYR A 682 " pdb=" C TYR A 682 " pdb=" CB TYR A 682 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR D 682 " pdb=" N TYR D 682 " pdb=" C TYR D 682 " pdb=" CB TYR D 682 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 6205 not shown) Planarity restraints: 6784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 682 " 0.030 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR D 682 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR D 682 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 682 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 682 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 682 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 682 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 682 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 682 " -0.030 2.00e-02 2.50e+03 2.43e-02 1.19e+01 pdb=" CG TYR C 682 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR C 682 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 682 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 682 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 682 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 682 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 682 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 682 " 0.030 2.00e-02 2.50e+03 2.43e-02 1.19e+01 pdb=" CG TYR A 682 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A 682 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 682 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 682 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 682 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 682 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 682 " 0.003 2.00e-02 2.50e+03 ... (remaining 6781 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1103 2.65 - 3.21: 43460 3.21 - 3.77: 62094 3.77 - 4.34: 79218 4.34 - 4.90: 119427 Nonbonded interactions: 305302 Sorted by model distance: nonbonded pdb=" O LEU A 653 " pdb=" OG SER A 656 " model vdw 2.087 2.440 nonbonded pdb=" O LEU C 653 " pdb=" OG SER C 656 " model vdw 2.087 2.440 nonbonded pdb=" O LEU D 653 " pdb=" OG SER D 656 " model vdw 2.087 2.440 nonbonded pdb=" O LEU B 653 " pdb=" OG SER B 656 " model vdw 2.087 2.440 nonbonded pdb=" OG1 THR D1347 " pdb=" O GLY D1390 " model vdw 2.105 2.440 ... (remaining 305297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 17.480 Check model and map are aligned: 0.090 Set scattering table: 0.380 Process input model: 97.380 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 124.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.085 38700 Z= 0.652 Angle : 0.891 11.171 52912 Z= 0.477 Chirality : 0.046 0.176 6208 Planarity : 0.005 0.041 6784 Dihedral : 13.827 87.363 12956 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 0.67 % Allowed : 12.02 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.09), residues: 5168 helix: -3.01 (0.07), residues: 2660 sheet: -3.24 (0.22), residues: 408 loop : -4.05 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 835 HIS 0.007 0.002 HIS A 283 PHE 0.017 0.003 PHE A 939 TYR 0.059 0.003 TYR C 682 ARG 0.005 0.001 ARG B 886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8848 (mtm) cc_final: 0.8371 (mpp) REVERT: A 619 MET cc_start: 0.8420 (ptm) cc_final: 0.8218 (ptm) REVERT: A 844 MET cc_start: 0.9166 (mmp) cc_final: 0.8928 (mmt) REVERT: A 1314 HIS cc_start: 0.7889 (t70) cc_final: 0.7498 (m170) REVERT: A 1365 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7108 (ptt90) REVERT: B 158 MET cc_start: 0.9444 (mtp) cc_final: 0.9203 (mtp) REVERT: C 122 MET cc_start: 0.8848 (mtm) cc_final: 0.8370 (mpp) REVERT: C 844 MET cc_start: 0.9164 (mmp) cc_final: 0.8930 (mmt) REVERT: C 1314 HIS cc_start: 0.7883 (t70) cc_final: 0.7496 (m170) REVERT: C 1365 ARG cc_start: 0.7296 (mtt90) cc_final: 0.7022 (ptt-90) REVERT: D 122 MET cc_start: 0.8682 (mtm) cc_final: 0.8473 (mpp) REVERT: D 215 MET cc_start: 0.8638 (mtm) cc_final: 0.8374 (mpp) REVERT: D 1314 HIS cc_start: 0.7845 (t70) cc_final: 0.7515 (m170) outliers start: 23 outliers final: 12 residues processed: 215 average time/residue: 0.4312 time to fit residues: 161.6224 Evaluate side-chains 173 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1451 ASP Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 1451 ASP Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 1451 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 407 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 472 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 537 GLN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS A 846 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 HIS A1437 ASN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 537 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS B 802 ASN B 846 GLN B 953 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1314 HIS ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 537 GLN ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 HIS C 846 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 HIS ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 537 GLN ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 HIS D 802 ASN D 846 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1314 HIS D1437 ASN ** D1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 38700 Z= 0.361 Angle : 0.687 7.595 52912 Z= 0.355 Chirality : 0.042 0.194 6208 Planarity : 0.004 0.040 6784 Dihedral : 5.355 43.473 5523 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 1.73 % Allowed : 17.43 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.11), residues: 5168 helix: -0.83 (0.09), residues: 2716 sheet: -2.99 (0.23), residues: 400 loop : -3.59 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1063 HIS 0.006 0.001 HIS B1068 PHE 0.024 0.002 PHE B 813 TYR 0.025 0.002 TYR C 682 ARG 0.003 0.000 ARG C1357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 MET cc_start: 0.8270 (ptm) cc_final: 0.8043 (ptm) REVERT: A 844 MET cc_start: 0.9067 (mmp) cc_final: 0.8820 (mmt) REVERT: A 1314 HIS cc_start: 0.7815 (t-90) cc_final: 0.7472 (m170) REVERT: B 122 MET cc_start: 0.8736 (mpp) cc_final: 0.8472 (mpp) REVERT: C 844 MET cc_start: 0.9068 (mmp) cc_final: 0.8824 (mmt) REVERT: C 1314 HIS cc_start: 0.7812 (t-90) cc_final: 0.7471 (m170) REVERT: D 215 MET cc_start: 0.8650 (mtm) cc_final: 0.8440 (mpp) REVERT: D 1125 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: D 1314 HIS cc_start: 0.7780 (t-90) cc_final: 0.7498 (m170) outliers start: 59 outliers final: 43 residues processed: 246 average time/residue: 0.4142 time to fit residues: 180.0698 Evaluate side-chains 221 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1451 ASP Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1451 ASP Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 908 LEU Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 393 optimal weight: 0.0470 chunk 321 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 473 optimal weight: 2.9990 chunk 511 optimal weight: 10.0000 chunk 421 optimal weight: 1.9990 chunk 469 optimal weight: 7.9990 chunk 161 optimal weight: 0.0670 chunk 379 optimal weight: 30.0000 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 346 ASN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 346 ASN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 38700 Z= 0.165 Angle : 0.575 6.788 52912 Z= 0.293 Chirality : 0.040 0.214 6208 Planarity : 0.004 0.040 6784 Dihedral : 4.693 26.101 5519 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.93 % Allowed : 18.36 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 5168 helix: 0.66 (0.10), residues: 2740 sheet: -2.63 (0.21), residues: 440 loop : -3.07 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 642 HIS 0.009 0.001 HIS D1068 PHE 0.040 0.001 PHE C1035 TYR 0.015 0.001 TYR A1074 ARG 0.007 0.000 ARG D 896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 218 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8905 (mtm) cc_final: 0.8476 (mpp) REVERT: A 680 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8259 (pp20) REVERT: A 844 MET cc_start: 0.9018 (mmp) cc_final: 0.8756 (mmt) REVERT: A 1314 HIS cc_start: 0.7805 (t-90) cc_final: 0.7480 (m170) REVERT: A 1502 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6257 (p90) REVERT: B 122 MET cc_start: 0.8800 (mpp) cc_final: 0.8538 (mpp) REVERT: B 680 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: B 1158 MET cc_start: 0.8741 (mmp) cc_final: 0.8429 (mmm) REVERT: B 1502 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6367 (p90) REVERT: C 122 MET cc_start: 0.8905 (mtm) cc_final: 0.8476 (mpp) REVERT: C 680 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (pp20) REVERT: C 844 MET cc_start: 0.9016 (mmp) cc_final: 0.8756 (mmt) REVERT: C 1314 HIS cc_start: 0.7802 (t-90) cc_final: 0.7480 (m170) REVERT: C 1502 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6245 (p90) REVERT: D 158 MET cc_start: 0.9542 (mtp) cc_final: 0.9310 (mtp) REVERT: D 680 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: D 1314 HIS cc_start: 0.7826 (t-90) cc_final: 0.7565 (m170) outliers start: 66 outliers final: 40 residues processed: 273 average time/residue: 0.4386 time to fit residues: 208.5010 Evaluate side-chains 240 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1377 VAL Chi-restraints excluded: chain D residue 1453 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 8.9990 chunk 355 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 474 optimal weight: 5.9990 chunk 502 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38700 Z= 0.238 Angle : 0.589 9.448 52912 Z= 0.297 Chirality : 0.040 0.146 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.504 22.226 5511 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.87 % Allowed : 19.27 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 5168 helix: 0.94 (0.10), residues: 2752 sheet: -2.47 (0.21), residues: 440 loop : -2.90 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1355 HIS 0.007 0.001 HIS B1068 PHE 0.029 0.001 PHE B 813 TYR 0.017 0.001 TYR A 682 ARG 0.009 0.000 ARG D1311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 198 time to evaluate : 4.802 Fit side-chains REVERT: A 122 MET cc_start: 0.8890 (mtm) cc_final: 0.8483 (mpp) REVERT: A 844 MET cc_start: 0.9035 (mmp) cc_final: 0.8806 (mmt) REVERT: A 1314 HIS cc_start: 0.7773 (t-90) cc_final: 0.7459 (m170) REVERT: A 1365 ARG cc_start: 0.7365 (mtt90) cc_final: 0.6906 (ptt-90) REVERT: A 1371 MET cc_start: 0.7966 (mmt) cc_final: 0.7728 (mmt) REVERT: A 1502 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6243 (p90) REVERT: B 122 MET cc_start: 0.8779 (mpp) cc_final: 0.8495 (mpp) REVERT: B 680 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8107 (pp20) REVERT: B 1125 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: B 1158 MET cc_start: 0.8753 (mmp) cc_final: 0.8480 (mmm) REVERT: B 1502 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6147 (p90) REVERT: C 122 MET cc_start: 0.8891 (mtm) cc_final: 0.8485 (mpp) REVERT: C 844 MET cc_start: 0.9034 (mmp) cc_final: 0.8807 (mmt) REVERT: C 1314 HIS cc_start: 0.7771 (t-90) cc_final: 0.7458 (m170) REVERT: C 1371 MET cc_start: 0.7968 (mmt) cc_final: 0.7729 (mmt) REVERT: C 1502 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6238 (p90) REVERT: D 680 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8119 (pp20) REVERT: D 931 MET cc_start: 0.7578 (ttt) cc_final: 0.7337 (ttm) REVERT: D 1125 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: D 1314 HIS cc_start: 0.7811 (t-90) cc_final: 0.7544 (m170) outliers start: 98 outliers final: 61 residues processed: 290 average time/residue: 0.4147 time to fit residues: 215.2440 Evaluate side-chains 259 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 191 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1377 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 428 optimal weight: 4.9990 chunk 347 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 451 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38700 Z= 0.255 Angle : 0.592 8.197 52912 Z= 0.299 Chirality : 0.040 0.162 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.451 22.061 5511 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.19 % Allowed : 20.47 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 5168 helix: 1.16 (0.10), residues: 2724 sheet: -2.34 (0.21), residues: 440 loop : -2.75 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 743 HIS 0.007 0.001 HIS B1068 PHE 0.025 0.001 PHE B1035 TYR 0.018 0.001 TYR B 682 ARG 0.004 0.000 ARG D1311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 198 time to evaluate : 4.213 Fit side-chains REVERT: A 122 MET cc_start: 0.8867 (mtm) cc_final: 0.8636 (mpp) REVERT: A 680 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 747 LEU cc_start: 0.9382 (pt) cc_final: 0.9162 (pt) REVERT: A 844 MET cc_start: 0.9031 (mmp) cc_final: 0.8795 (mmt) REVERT: A 1314 HIS cc_start: 0.7741 (t-90) cc_final: 0.7438 (m170) REVERT: A 1502 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6251 (p90) REVERT: B 122 MET cc_start: 0.8769 (mpp) cc_final: 0.8470 (mpp) REVERT: B 1125 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: B 1158 MET cc_start: 0.8759 (mmp) cc_final: 0.8511 (mmm) REVERT: B 1502 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6160 (p90) REVERT: C 122 MET cc_start: 0.8872 (mtm) cc_final: 0.8641 (mpp) REVERT: C 680 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: C 747 LEU cc_start: 0.9380 (pt) cc_final: 0.9160 (pt) REVERT: C 844 MET cc_start: 0.9031 (mmp) cc_final: 0.8797 (mmt) REVERT: C 1314 HIS cc_start: 0.7741 (t-90) cc_final: 0.7437 (m170) REVERT: C 1371 MET cc_start: 0.8007 (mmt) cc_final: 0.7786 (mmt) REVERT: C 1502 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6249 (p90) REVERT: D 1314 HIS cc_start: 0.7810 (t-90) cc_final: 0.7530 (m170) outliers start: 109 outliers final: 73 residues processed: 303 average time/residue: 0.3866 time to fit residues: 210.7285 Evaluate side-chains 275 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 196 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1377 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 30.0000 chunk 452 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 124 optimal weight: 50.0000 chunk 503 optimal weight: 50.0000 chunk 417 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 264 optimal weight: 50.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 684 HIS ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 HIS C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1241 ASN ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 GLN D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 38700 Z= 0.484 Angle : 0.735 8.705 52912 Z= 0.374 Chirality : 0.043 0.258 6208 Planarity : 0.004 0.041 6784 Dihedral : 4.838 23.259 5511 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.71 % Allowed : 22.34 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 5168 helix: 0.62 (0.10), residues: 2760 sheet: -2.50 (0.21), residues: 460 loop : -2.76 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 835 HIS 0.007 0.002 HIS D1068 PHE 0.023 0.002 PHE B 813 TYR 0.025 0.002 TYR D 682 ARG 0.005 0.001 ARG C 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 193 time to evaluate : 4.873 Fit side-chains REVERT: A 122 MET cc_start: 0.8859 (mtm) cc_final: 0.8335 (mpp) REVERT: A 844 MET cc_start: 0.9077 (mmp) cc_final: 0.8821 (mmt) REVERT: A 931 MET cc_start: 0.7622 (ttt) cc_final: 0.7353 (ttm) REVERT: A 1314 HIS cc_start: 0.7782 (t-90) cc_final: 0.7442 (m170) REVERT: A 1371 MET cc_start: 0.7677 (mmt) cc_final: 0.7475 (mmt) REVERT: A 1502 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6307 (p90) REVERT: B 122 MET cc_start: 0.8758 (mpp) cc_final: 0.8468 (mpp) REVERT: B 832 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8831 (mt) REVERT: B 1502 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6282 (p90) REVERT: C 122 MET cc_start: 0.8860 (mtm) cc_final: 0.8334 (mpp) REVERT: C 844 MET cc_start: 0.9078 (mmp) cc_final: 0.8823 (mmt) REVERT: C 1314 HIS cc_start: 0.7779 (t-90) cc_final: 0.7440 (m170) REVERT: C 1502 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6423 (p90) REVERT: D 931 MET cc_start: 0.7652 (ttt) cc_final: 0.7377 (ttm) REVERT: D 1158 MET cc_start: 0.8873 (mmp) cc_final: 0.8398 (mmm) REVERT: D 1314 HIS cc_start: 0.7826 (t-90) cc_final: 0.7494 (m-70) outliers start: 127 outliers final: 84 residues processed: 318 average time/residue: 0.4080 time to fit residues: 233.5433 Evaluate side-chains 275 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 187 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 367 optimal weight: 0.9990 chunk 284 optimal weight: 7.9990 chunk 423 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 501 optimal weight: 20.0000 chunk 313 optimal weight: 0.9980 chunk 305 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 38700 Z= 0.161 Angle : 0.583 9.555 52912 Z= 0.292 Chirality : 0.039 0.140 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.363 20.889 5511 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.75 % Allowed : 23.45 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 5168 helix: 1.42 (0.10), residues: 2720 sheet: -2.12 (0.21), residues: 444 loop : -2.53 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 642 HIS 0.007 0.001 HIS D1068 PHE 0.016 0.001 PHE D1035 TYR 0.011 0.001 TYR B 893 ARG 0.004 0.000 ARG D1311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 204 time to evaluate : 3.583 Fit side-chains REVERT: A 619 MET cc_start: 0.8107 (ptm) cc_final: 0.7875 (ptm) REVERT: A 844 MET cc_start: 0.9005 (mmp) cc_final: 0.8699 (mmt) REVERT: A 1158 MET cc_start: 0.8787 (mmp) cc_final: 0.8394 (mmm) REVERT: A 1314 HIS cc_start: 0.7784 (t-90) cc_final: 0.7450 (m-70) REVERT: A 1371 MET cc_start: 0.7738 (mmt) cc_final: 0.7349 (mmt) REVERT: A 1502 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.5649 (p90) REVERT: B 67 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8071 (tp) REVERT: B 122 MET cc_start: 0.8779 (mpp) cc_final: 0.8464 (mpp) REVERT: B 1502 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6076 (p90) REVERT: C 844 MET cc_start: 0.9002 (mmp) cc_final: 0.8699 (mmt) REVERT: C 931 MET cc_start: 0.7496 (ttt) cc_final: 0.7295 (ttm) REVERT: C 1158 MET cc_start: 0.8759 (mmp) cc_final: 0.8548 (mmm) REVERT: C 1314 HIS cc_start: 0.7781 (t-90) cc_final: 0.7460 (m-70) REVERT: C 1371 MET cc_start: 0.7530 (mmt) cc_final: 0.7226 (mmt) REVERT: C 1502 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6025 (p90) REVERT: D 1314 HIS cc_start: 0.7819 (t-90) cc_final: 0.7521 (m-70) outliers start: 94 outliers final: 65 residues processed: 297 average time/residue: 0.3966 time to fit residues: 210.5027 Evaluate side-chains 262 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 193 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1363 ILE Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 299 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 318 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38700 Z= 0.280 Angle : 0.616 10.336 52912 Z= 0.307 Chirality : 0.040 0.171 6208 Planarity : 0.004 0.039 6784 Dihedral : 4.386 22.125 5511 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.54 % Allowed : 24.33 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 5168 helix: 1.36 (0.10), residues: 2720 sheet: -2.21 (0.21), residues: 460 loop : -2.46 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 743 HIS 0.007 0.001 HIS A1068 PHE 0.034 0.002 PHE B 813 TYR 0.017 0.001 TYR D 682 ARG 0.003 0.000 ARG D 929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 193 time to evaluate : 4.431 Fit side-chains REVERT: A 844 MET cc_start: 0.9058 (mmp) cc_final: 0.8771 (mmt) REVERT: A 1158 MET cc_start: 0.8803 (mmp) cc_final: 0.8480 (mmm) REVERT: A 1314 HIS cc_start: 0.7794 (t-90) cc_final: 0.7446 (m170) REVERT: A 1371 MET cc_start: 0.7833 (mmt) cc_final: 0.7622 (mmt) REVERT: A 1502 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6141 (p90) REVERT: B 122 MET cc_start: 0.8779 (mpp) cc_final: 0.8462 (mpp) REVERT: B 1502 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6100 (p90) REVERT: C 844 MET cc_start: 0.9057 (mmp) cc_final: 0.8771 (mmt) REVERT: C 931 MET cc_start: 0.7589 (ttt) cc_final: 0.7327 (ttm) REVERT: C 1314 HIS cc_start: 0.7791 (t-90) cc_final: 0.7472 (m170) REVERT: C 1371 MET cc_start: 0.7670 (mmt) cc_final: 0.7441 (mmt) REVERT: C 1502 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6045 (p90) REVERT: D 1314 HIS cc_start: 0.7834 (t-90) cc_final: 0.7518 (m-70) outliers start: 87 outliers final: 72 residues processed: 280 average time/residue: 0.4051 time to fit residues: 203.0538 Evaluate side-chains 264 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 189 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 2.9990 chunk 480 optimal weight: 0.8980 chunk 438 optimal weight: 0.9990 chunk 467 optimal weight: 30.0000 chunk 281 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 366 optimal weight: 0.0470 chunk 143 optimal weight: 2.9990 chunk 422 optimal weight: 10.0000 chunk 441 optimal weight: 0.0670 chunk 465 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 38700 Z= 0.147 Angle : 0.582 12.695 52912 Z= 0.285 Chirality : 0.039 0.257 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.148 21.209 5511 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.05 % Allowed : 24.71 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 5168 helix: 1.63 (0.10), residues: 2728 sheet: -1.87 (0.22), residues: 444 loop : -2.40 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 944 HIS 0.007 0.001 HIS D1068 PHE 0.016 0.001 PHE B 813 TYR 0.010 0.001 TYR B 893 ARG 0.004 0.000 ARG D1311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 4.320 Fit side-chains revert: symmetry clash REVERT: A 619 MET cc_start: 0.8096 (ptm) cc_final: 0.7861 (ptm) REVERT: A 844 MET cc_start: 0.8990 (mmp) cc_final: 0.8673 (mmt) REVERT: A 1158 MET cc_start: 0.8745 (mmp) cc_final: 0.8458 (mmm) REVERT: A 1314 HIS cc_start: 0.7804 (t-90) cc_final: 0.7478 (m170) REVERT: A 1371 MET cc_start: 0.7972 (mmt) cc_final: 0.7642 (mmt) REVERT: A 1502 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.5734 (p90) REVERT: B 67 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 122 MET cc_start: 0.8728 (mpp) cc_final: 0.8433 (mpp) REVERT: B 1502 HIS cc_start: 0.6833 (OUTLIER) cc_final: 0.5863 (p90) REVERT: C 844 MET cc_start: 0.8988 (mmp) cc_final: 0.8674 (mmt) REVERT: C 931 MET cc_start: 0.7524 (ttt) cc_final: 0.7267 (ttm) REVERT: C 1314 HIS cc_start: 0.7782 (t-90) cc_final: 0.7456 (m170) REVERT: C 1371 MET cc_start: 0.7761 (mmt) cc_final: 0.7347 (mmt) REVERT: C 1502 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.5673 (p90) REVERT: D 67 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8081 (tp) REVERT: D 1314 HIS cc_start: 0.7825 (t-90) cc_final: 0.7536 (m170) outliers start: 70 outliers final: 50 residues processed: 277 average time/residue: 0.4265 time to fit residues: 209.3934 Evaluate side-chains 251 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 196 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 647 ASP Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 2.9990 chunk 493 optimal weight: 40.0000 chunk 301 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 518 optimal weight: 20.0000 chunk 476 optimal weight: 7.9990 chunk 412 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38700 Z= 0.265 Angle : 0.622 13.116 52912 Z= 0.306 Chirality : 0.040 0.175 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.214 22.033 5511 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.99 % Allowed : 24.97 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 5168 helix: 1.56 (0.10), residues: 2724 sheet: -1.85 (0.22), residues: 440 loop : -2.33 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1355 HIS 0.006 0.001 HIS A1068 PHE 0.029 0.001 PHE B1035 TYR 0.016 0.001 TYR D 682 ARG 0.004 0.000 ARG D1311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 198 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 844 MET cc_start: 0.9037 (mmp) cc_final: 0.8738 (mmt) REVERT: A 1314 HIS cc_start: 0.7808 (t-90) cc_final: 0.7451 (m170) REVERT: A 1371 MET cc_start: 0.7974 (mmt) cc_final: 0.7645 (mmt) REVERT: A 1502 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.5768 (p90) REVERT: B 122 MET cc_start: 0.8761 (mpp) cc_final: 0.8465 (mpp) REVERT: B 1502 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.5957 (p90) REVERT: C 844 MET cc_start: 0.9036 (mmp) cc_final: 0.8739 (mmt) REVERT: C 931 MET cc_start: 0.7643 (ttt) cc_final: 0.7366 (ttm) REVERT: C 1314 HIS cc_start: 0.7801 (t-90) cc_final: 0.7476 (m170) REVERT: C 1371 MET cc_start: 0.7771 (mmt) cc_final: 0.7363 (mmt) REVERT: C 1502 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.5722 (p90) REVERT: D 1314 HIS cc_start: 0.7848 (t-90) cc_final: 0.7540 (m170) outliers start: 68 outliers final: 56 residues processed: 266 average time/residue: 0.4552 time to fit residues: 213.1436 Evaluate side-chains 256 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1502 HIS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1453 ASN Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1502 HIS Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1453 ASN Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain C residue 1502 HIS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 380 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 413 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.068743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048465 restraints weight = 250692.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050009 restraints weight = 135145.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050983 restraints weight = 93738.988| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38700 Z= 0.204 Angle : 0.603 12.789 52912 Z= 0.295 Chirality : 0.039 0.172 6208 Planarity : 0.004 0.039 6784 Dihedral : 4.168 21.654 5511 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.02 % Allowed : 24.97 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 5168 helix: 1.62 (0.10), residues: 2724 sheet: -1.78 (0.22), residues: 444 loop : -2.29 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1355 HIS 0.007 0.001 HIS D1068 PHE 0.035 0.001 PHE B1035 TYR 0.013 0.001 TYR B 682 ARG 0.009 0.000 ARG D1357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5768.37 seconds wall clock time: 106 minutes 59.61 seconds (6419.61 seconds total)